Importance of an Astrophysical Perspective for Textbook Relativity

The importance of a teaching a clear definition of the ``observer'' in special relativity is highlighted using a simple astrophysical example from the exciting current research area of ``Gamma-Ray Burst'' astrophysics. The example shows that a source moving relativistically toward a single observer at rest exhibits a time ``contraction'' rather than a ``dilation'' because the light travel time between the source and observer decreases with time. Astrophysical applications of special relativity complement idealized examples with real applications and very effectively exemplify the role of a finite light travel time.Comment: 5 pages TeX, European Journal of Physics, in pres

ABC transporters: the power to change

ATP-binding cassette (ABC) transporters constitute a ubiquitous superfamily of integral membrane proteins that are responsible for the ATP-powered translocation of many substrates across membranes. The highly conserved ABC domains of ABC transporters provide the nucleotide-dependent engine that drives transport. By contrast, the transmembrane domains that create the translocation pathway are more variable. Recent structural advances with prokaryotic ABC transporters have provided a qualitative molecular framework for deciphering the transport cycle. An important goal is to develop quantitative models that detail the kinetic and molecular mechanisms by which ABC transporters couple the binding and hydrolysis of ATP to substrate translocation

Homographically generated light sheets for the microscopy of large specimens.

We compare the performance of linear and nonlinear methods for aligning the excitation and detection planes throughout volumes of large specimens in digitally scanned light sheet microscopy. An effective nonlinear method involves the registration of four corner extrema of the imaging volume via a projective transform. We show that this improves the light collection efficiency of the commonly used three-point affine registration by an average of 42% over a typical specimen volume. Accurate illumination/detection registration methods are now pertinent to biological research in view of current trends towards imaging large or expanded samples, at depth, with diffraction limited resolution

Ellipsoid Localisation Microscopy

Multilayered protein coats are crucial to the dormancy, robustness, and germination of bacterial spores. In Bacillus subtilis spores, the coat contains over 70 distinct proteins. Identifying which proteins reside in each layer may provide insight into their distinct functions. We present image analysis methods that determine the order and geometry of concentric protein layers by fitting a model description for a spheroidal fluorescent shell image to optical micrographs of spores incorporating fluorescent fusion proteins. The radius of a spherical protein shell can be determined with <10 nm error by fitting an equation to widefield fluorescence micrographs. Ellipsoidal shell axes can be fitted with comparable precision. The layer orders inferred for B. subtilis and B. megaterium are consistent with measurements in the literature. The aspect ratio of elongated spores and the tendency of some proteins to localize near their poles can be quantified, enabling measurement of structural anisotropy.We gratefully acknowledge support from MedImmune through the Beacon collaboration, the EPSRC Centre for Doctoral Training in Sensor Technologies and Applications (EP/L015889/1), and thank Clemens Kaminski, Romain Laine and Jose Casas-Finet for inspiring discussions.This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.bpj.2015.09.02

Novel cortex lytic enzymes in Bacillus megaterium QM B1551 spores.

Present models for spore germination in Bacillus species include a requirement for either the SleB or CwlJ cortex lytic enzymes to efficiently depolymerise the spore cortex. Previous work has demonstrated that B. megaterium spores may differ to other species in this regard, since sleB cwlJ null mutant spores complemented with the gene in trans for the non-peptidoglycan lysin YpeB can efficiently degrade the cortex. Here, we identify two novel cortex lytic enzymes, encoded at the BMQ_2391 and BMQ_3234 loci, which are essential for cortex hydrolysis in the absence of SleB and CwlJ. Ellipsoid localisation microscopy places the BMQ_3234 protein within the inner-spore coat, a region of the spore that is populated by other cortex lytic enzymes. The findings reinforce the idea that there is a degree of variation in mechanisms of cortex hydrolysis across the Bacillales, raising potential implications for environmental decontamination strategies based upon targeted inactivation of components of the spore germination apparatus.BAR was the recipient of a scholarship from the Sultanate of Oman government. AG was the recipient of a Cambridge Nehru Scholarship and received support from the Raymond and Beverly Sackler Foundation

The Expected Rate of Gamma-Ray Burst Afterglows In Supernova Searches

We predict the rate at which Gamma-Ray Burst (GRB) afterglows should be detected in supernova searches as a function of limiting flux. Although GRB afterglows are rarer than supernovae, they are detectable at greater distances because of their higher intrinsic luminosity. Assuming that GRBs trace the cosmic star formation history and that every GRB gives rise to a bright afterglow, we find that the average detection rate of supernovae and afterglows should be comparable at limiting magnitudes brighter than K=18. The actual rate of afterglows is expected to be somewhat lower since only a fraction of all gamma-ray selected GRBs were observed to have associated afterglows. However, the rate could also be higher if the initial gamma-ray emission from GRB sources is more beamed than their late afterglow emission. Hence, current and future supernova searches can place strong constraints on the afterglow appearance fraction and the initial beaming angle of GRB sources.Comment: 13 pages, submitted to ApJ

First recorded occurrence of the parasitic barnacle (Anelasma squalicola) on a Greenland shark (Somniosus microcephalus) in the Canadian Arctic

A solitary Anelasma squalicola specimen was collected from the cloaca of a Greenland shark (Somniosus microcephalus), the first time this association has been recorded. The specimen's identity was confirmed through morphological and genetic assessment (mitochondrial markers: COI and control region). A. squalicola is a species typically associated with deep-sea lantern sharks (Etmopteridae) and, until the present observation, had never been observed at a sexually mature size in the absence of a mating partner. Given the reported negative effects of this parasite on its hosts, monitoring Greenland sharks for additional cases is recommended.publishedVersio